hotspotter.variable: Find hotspots of genomic events
In AneuFinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Description Usage Arguments Details Value Author(s)

Find hotspots of genomic events by using kernel density estimation.

1	hotspotter.variable(breakpoints, confint, pval = 0.05, spacing.bp = 5000)

`breakpoints`	A list with `GRanges-class` object containing the coordinates of the genomic events and their confidence intervals.
`confint`	Confidence interval that was used for breakpoint estimation.
`pval`	P-value cutoff for hotspots.
`spacing.bp`	Spacing of datapoints for KDE in basepairs.

The hotspotter uses a gaussian kernel with variable bandwidth to perform a KDE. The bandwidth depends on the confidence intervals of the breakpoints. A p-value is calculated by comparing the density profile of the genomic events with the density profile of a randomly subsampled set of genomic events (bootstrapping).

A list of GRanges-class objects containing 1) coordinates of hotspots and 2) p-values within the hotspot.

Aaron Taudt

AneuFinder documentation built on Nov. 8, 2020, 7:44 p.m.